Figure 4

Tumor ploidy and percentage of aberrant tumor cells in HER2-amplified compared to HER2-negative breast cancer. (A) Distribution of FCM-ploidy across PAM50 subtypes for 260 cases with concurrent gene expression data. Of the 34 HER2-enriched cases, 21 had concurrent BAC aCGH data. 19 of these 21 cases showed amplification of HER2 by BAC aCGH, (B) Distribution of FCM-ploidy across 219 breast cancer samples grouped as HER2-amplified by BAC aCGH, or HER2-negative by BAC aCGH and further stratified by PAM50 subtype. (C) Distribution of FCM-ploidy for 84 HER2-amplified cases stratified by ER-status. (D) Distribution of percentage of aberrant cells estimated by GAP analysis of 407 breast cancers across HER2-amplified tumors and HER2-negative tumors stratified by PAM50 subtypes and ER-status. A significant difference in aberrant cell estimates is observed between HER2-amplified and HER2-negative cases stratified by PAM50 subtype (P = 0.003, ANOVA). A similar difference was observed when comparing aberrant cell estimates for all HER2-amplified tumors against HER2-negative cases stratified by PAM50 subtype (P = 0.02, ANOVA). In A to C, curves were generated by an Epanechnikov smoothing kernel with 0.08 smoothing bandwidth.